title: Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.
abstract: To understand how cell physiological state affects mRNA translation, we used Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein-mRNA ratios were primarily due to differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Transcription levels were sp. significantly altered for 26% of the protein changes; translational efficiency was significantly altered for 46% and a combination of both was responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part due to altered tRNA pools, is a major determinant of regulated alterations in protein expression levels in bacteria.
authors.affiliation: Computational Biosciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
authors.forename: Ronald C
authors.initials: RC
authors.lastname: Taylor
authors.forename: Bobbie-Jo M
authors.initials: BJ
authors.lastname: Webb Robertson
authors.forename: Lye Meng
authors.initials: LM
authors.lastname: Markillie
authors.forename: Margrethe H
authors.initials: MH
authors.lastname: Serres
authors.forename: Bryan E
authors.initials: BE
authors.lastname: Linggi
authors.forename: Joshua T
authors.initials: JT
authors.lastname: Aldrich
authors.forename: Eric A
authors.initials: EA
authors.lastname: Hill
authors.forename: Margaret F
authors.initials: MF
authors.lastname: Romine
authors.forename: Mary S
authors.initials: MS
authors.lastname: Lipton
authors.forename: H Steven
authors.initials: HS
authors.lastname: Wiley
mesh_terms: D018407:Bacterial Physiological Phenomena; D001426:Bacterial Proteins / Q000378:metabolism; D003062:Codon; D004777:Environment; D004926:Escherichia coli / Q000378:metabolism; D013058:Mass Spectrometry; D010100:Oxygen / Q000378:metabolism; D014176:Protein Biosynthesis; D020543:Proteome; D040901:Proteomics; D012333:RNA, Messenger / Q000378:metabolism; D012343:RNA, Transfer / Q000378:metabolism; D012044:Regression Analysis; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA; D020592:Shewanella / Q000235:genetics* / Q000378:metabolism*; D013997:Time Factors; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D020543:Proteome; D012333:RNA, Messenger; D012343:RNA, Transfer; D010100:Oxygen